Variant report

Variant	rs1498273
Chromosome Location	chr10:4728091-4728092
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:4726532..4729778-chr10:4736353..4738324,3	MCF-7	breast:
2	chr10:4724736..4726805-chr10:4727300..4730027,2	MCF-7	breast:
3	chr10:4721349..4725146-chr10:4726234..4729626,7	MCF-7	breast:
4	chr10:4717810..4723074-chr10:4727723..4730891,5	MCF-7	breast:
5	chr10:4727830..4729857-chr10:4775467..4777003,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231298	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11252656	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11252657	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11252658	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11252660	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11252662	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12572602	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498272	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17133411	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242771	0.80[ASN][1000 genomes]
rs4992184	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7080649	0.82[ASN][1000 genomes]
rs924288	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894787	chr10:4385379-4857717	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv1798456	chr10:4689138-4731081	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1817443	chr10:4689138-4731081	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1831014	chr10:4689138-4731081	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv1838419	chr10:4689138-4731081	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1498273	NET1	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4721200-4728400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr10:4721200-4729000	Weak transcription	NHDF-Ad	bronchial
3	chr10:4721200-4733600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr10:4725600-4728800	Enhancers	A549	lung
5	chr10:4725800-4728400	Enhancers	HMEC	breast
6	chr10:4725800-4729000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:4725800-4730000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr10:4725800-4730800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr10:4726000-4728200	Enhancers	NHEK	skin
10	chr10:4726000-4730800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:4726400-4729000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr10:4726600-4728200	Enhancers	NH-A	brain
13	chr10:4726600-4728200	Weak transcription	Osteobl	bone
14	chr10:4726600-4728800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr10:4727000-4728200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr10:4727000-4728200	Enhancers	Fetal Muscle Leg	muscle
17	chr10:4727000-4728400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr10:4727000-4728600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr10:4727000-4730000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr10:4727000-4731200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr10:4727200-4728200	Enhancers	Psoas Muscle	Psoas
22	chr10:4727200-4728200	Enhancers	HUVEC	blood vessel
23	chr10:4727200-4728400	Enhancers	Placenta Amnion	Placenta Amnion
24	chr10:4727200-4733800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr10:4727400-4729600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr10:4727800-4728200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr10:4727800-4728200	Enhancers	Fetal Muscle Trunk	muscle
28	chr10:4727800-4728400	Enhancers	Adipose Nuclei	Adipose
29	chr10:4727800-4728400	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr10:4727800-4729200	Enhancers	HSMM	muscle
31	chr10:4727800-4730000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr10:4728000-4728400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr10:4728000-4728400	Enhancers	Pancreas	Pancrea
34	chr10:4728000-4728600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr10:4728000-4728800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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